The new 2009 are common rail. Before that they were pump deuse starting 2004 for the sedan and 2003 for the wagon. 1996-2003 TDIs have bosch ve rotary pumps which can be converted to mechanical injection so you can do without the ECU.
I don't know about the price. On ebay, the cheapest TDI engine is $1700. But I would be happy to sell my current TDI with a perfectly working powertrain for $1500. There are quite a few of rusted through 1997-1999 TDIs around here with very solid powertrains.
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